Atopic dermatitis (AD) is a complex disease with a firmly established genetic underpinning. Altered skin colonization by Staphylococcus aureus is common in AD and is associated with disease severity, but not all AD patients are colonized. Keratinocytes, which constitute 85% of the cells of the epidermis, the first line of defense in the skin, play a central role in AD pathogenesis. Increased susceptibility to infections and cutaneous colonization suggest immune dysregulation and skin barrier dysfunction where genetic variation is very likely to play a role. Genes in these pathways have been implicated by genome wide association studies (GWAS) of AD, but genetic studies focusing specifically on S. aureus colonization have yet to be performed. A cost- effective strategy to boost power in genetic association studies is to sequence a portion of a population and generate ?synthetic? genomes for the remaining samples by imputing the sequence data to the rest of the dataset genotyped on a genome-wide marker array. Through the NIAID-supported Atopic Dermatitis Research Network (ADRN), we have already completed whole genome sequencing (WGS) on 500 ADRN participants with/without persistent S. aureus colonization. As with other studies, most significant GWAS markers lie in intergenic or intronic regions, which may reflect regulatory variants. Expression quantitative trait loci (eQTL) represent one strategy to test if genome-wide marker panels can explain expression in the transcriptome, and control of gene expression is one way genetic variants might control risk to AD. The skin microbiota resists pathogens and educates the immune system, and the epidermis mediates this interface. We hypothesize interactions between the human host and symbiotic bacteria, when disrupted by genetic or environmental changes, can result in persistent S. aureus colonization among AD patients. To test this hypothesis, we will integrate one of the most comprehensive databases on S. aureus colonization among AD patients using RNA- Seq and eQTL mapping to elucidate genetic variation underpinning differences in levels of gene expression in the AD epidermis. Our specific aims include: (i) combine WGS data with genome-wide marker data to identify genetic variants influencing risk of S. aureus colonization and disease severity in 1,100 colonized and uncolonized AD patients; (ii) identify cis- and trans-effects of variants in the epidermis transcriptome of AD patients with S. aureus colonization by eQTL mapping; and (iii) examine the complex relationships between the host epithelial cell genome, the epidermal transcriptome and the functionally profiled microbiome to characterize the human-commensal interaction in S. aureus colonization of AD. We will also determine whether genetic and/or genomic (eQTL) determinants contribute to success of two clinical trials in this U19 application: (i) the microbiome transplant to decrease S. aureus colonization in AD (Microbiome Transplant protocol); and (ii) the dupilumab-induced reduction in S. aureus quantity (Dupilumab protocol). These studies will substantially advance our understanding of the molecular basis for S. aureus colonization and AD severity.